Here's a quick and dirty way to get the result set you show....
Create a query called "crossref" with this SQL
SELECT coco.*, types.*
FROM coco, types;
Create a second query with this SQL
SELECT crossref.refc, crossref.reft, Count(tools.reftool) AS Number
FROM tools RIGHT JOIN crossref ON (tools.reft = crossref.reft) AND (tools.refc = crossref.refc)
GROUP BY crossref.refc, crossref.reft;
It could probably be done with just one query, if you nested the first one
inside the second one....